add ppb concentrations to output

src/converter/PtrmsConverter.py

@@ -133,11 +133,11 @@ class PtrmsConverter(Converter.Converter):
         """
         # load data
         self.reader = AMESReader(infiles[0])
+        year = int(self.reader.attributes['Startdate'][0:4])
         ds_names = self.reader.get_ds_names()
         indata = Converter.Converter.load_indata(self, infiles, ds_names, reader_interface=AMESReader)
         
         self.var_ids_mz = []
-        self.var_ids_mz_name = []
         self.var_ids_env_tag = []
         self.var_ids_env = []
         
@@ -146,6 +146,8 @@ class PtrmsConverter(Converter.Converter):
                 indata[Product.START_ACQ_ID] = indata[var_id]
             elif 'end_time' in var_id:
                 indata[Product.END_ACQ_ID] = indata[var_id]
+            elif "status" in var_id:
+                indata["status"] = indata[var_id]
             elif "temperature" in var_id and "Location=inlet" in var_id:
                 self.var_ids_env.append(var_id)
                 self.var_ids_env_tag.append('T_inlet')
@@ -157,7 +159,6 @@ class PtrmsConverter(Converter.Converter):
                 if m != None:
                     mass_num = m.group(0).replace('_','')
                     indata['mz_' + mass_num] = indata[var_id]
-                    self.var_ids_mz_name.append(var_id)
                     self.var_ids_mz.append('mz_' + mass_num)
                 else:
                     if 'methanal' in var_id:
@@ -179,10 +180,16 @@ class PtrmsConverter(Converter.Converter):
                     indata['mz_' + mass_num] = indata[var_id]
                     self.var_ids_mz.append('mz_' + mass_num)
         
-        year = int(self.reader.attributes['Startdate'][0:4])
-
+        
+        # filtering from status values
+        valid_status = (indata['status'] == 0)
+        for var_id in indata.keys():
+            indata[var_id] = indata[var_id][valid_status]
+        
         # convert to ppm concentration
         prog_ptrms_lib = ptrms_lib(outdir, conf_file)
+        self.lev1_mz =prog_ptrms_lib.conf["cols_species"]
+        self.lev1_mz_name = [prog_ptrms_lib.conf["species"][s]["actris_name"] for s in prog_ptrms_lib.conf["cols_species"]]
         ppb_data, lod, rsd, accuracy, uncertainty = prog_ptrms_lib.process(indata, valve_files, outdir, levels=[0])
         
         # group outputs
@@ -216,7 +223,7 @@ class PtrmsConverter(Converter.Converter):
         i_sort = numpy.argsort(outdata[Product.START_ACQ_ID])
         outdata["start_acq"] = [outdata["start_acq"][i] for i in i_sort]
         outdata["end_acq"] = [outdata["end_acq"][i] for i in i_sort]
-        for var_id in self.var_ids_env + self.var_ids_mz:
+        for var_id in self.var_ids_env + self.lev1_mz:
             outdata[var_id] = [outdata[var_id][i] for i in i_sort]
             invalid_acq_val[var_id] = numpy.array(
                 [invalid_acq_val[var_id][i] for i in i_sort]
@@ -237,7 +244,7 @@ class PtrmsConverter(Converter.Converter):
             )
 
             # concentrations coef
-            for var_id in self.var_ids_env + self.var_ids_mz:
+            for var_id in self.var_ids_env + self.lev1_mz:
                 conc = outdata[var_id][i]
 
                 qa = 0.0
@@ -277,7 +284,7 @@ class PtrmsConverter(Converter.Converter):
         """
         if var_id == self.QA_FLAGS_ID:
             return 9.999
-        elif var_id in self.var_ids_mz:
+        elif var_id in self.lev1_mz:
             return self.var_fills_conc
         elif var_id in self.var_ids_env:
             return self.var_fills_env
@@ -296,7 +303,7 @@ class PtrmsConverter(Converter.Converter):
         infill = self.var_fills_conc_native
 
         # --- environmental property and concentration automatic QA
-        for var_id in self.var_ids_env + self.var_ids_mz:
+        for var_id in self.var_ids_env + self.lev1_mz:
             data = indata[var_id]
             # data = numpy.array([float(d.replace('E','e').replace(',','.')) for d in data])
             data = numpy.array(data)
@@ -336,7 +343,7 @@ class PtrmsConverter(Converter.Converter):
         nvars = 1  # end time
         nvars += 1  # status
         nvars += len(self.var_ids_env) * 2  # T, P and QA
-        nvars += len(self.var_ids_mz) * 2  # m/e and QA flag
+        nvars += len(self.lev1_mz) * 2  # m/e and QA flag
 
         return nvars
 
@@ -375,7 +382,7 @@ class PtrmsConverter(Converter.Converter):
         s += "9.999 "
         s += str(self.var_fills_conc) + " "  # P
         s += "9.999 "
-        for me in self.var_ids_mz:
+        for me in self.lev1_mz:
             s += str(self.var_fills_conc)
             s += " "
             s += "9.999 "
@@ -400,8 +407,8 @@ class PtrmsConverter(Converter.Converter):
         )
         vars_long_name += "numflag_pressure, no unit" + os.linesep
   
-        for var_id in self.var_ids_mz_name:
-            vars_long_name += var_id + os.linesep
+        for var_id in self.lev1_mz_name:
+            vars_long_name += var_id + ", ppb" + os.linesep
             vars_long_name += "numflag_" + var_id + ", no unit" + os.linesep
         vars_long_name = vars_long_name.strip()
 
@@ -413,7 +420,7 @@ class PtrmsConverter(Converter.Converter):
             vars_tag += "{0:<20s}".format(var_id)
             vars_tag += "{0:<20s}".format("numflag_" + var_id)
 
-        for var_id in self.var_ids_mz:
+        for var_id in self.lev1_mz:
             vars_tag += "{0:<20s}".format(var_id)
             vars_tag += "{0:<20s}".format(var_id + "_numflag")
         vars_tag = vars_tag.strip()

src/rawto012.py

@@ -117,7 +117,7 @@ def main():
 
 def test():
     SRC_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)),'..')
-    infile = SRC_DIR + "/tests/SIRTA/inputs/FR0020R.20241028000550.20250108081653.PTR-MS.ion_count.air.1d.5mn.FR01L_PTR-MS_Ionicon_Analytik_H-S-PTR-QMS.FR01L_Ionicon_Analytik_H-S-PTR-QMS_GIF.lev0.nas"
+    infile = SRC_DIR + "/tests/SIRTA/inputs/FR0020R.20241028000550.20250113125332.PTR-MS.ion_count.air.1d.5mn.FR01L_PTR-MS_Ionicon_Analytik_H-S-PTR-QMS.FR01L_Ionicon_Analytik_H-S-PTR-QMS_GIF.lev0.nas"
     conf_file = '/src/algo/ptrms_lib/conf/conf_ptrms.toml'
     valve_files = "/tests/SIRTA/inputs/vanne_pos_20241028.csv"
     outdir = SRC_DIR + "/tests/SIRTA/results/"